Command line interface

The command line interface for hiwenet (although I recommend using it via API) is shown below. Check the bottom of this page for examples.

A rough example of usage can be:

#!/bin/bash
#$ -l mf=4G -q abaqus.q -wd /work/project/PBS -j yes -o /work/project/output/job.log
cd /work/project/output
hiwenet -f thickness/features_1000.txt -g thickness/groups_1000.txt -w manhattan -n 50 -o thickness/hiwenet_manhatten_n50.csv

The default behaviour of hiwenet is to trim the outliers, as I suspect their existence in the feature distributions of different ROIs. But if you choose not to do it, you can disable it like this with -t False flag:

#!/bin/bash
#$ -l mf=4G -q abaqus.q -wd /work/project/PBS -j yes -o /work/project/output/job.log
cd /work/project/output
hiwenet -f thickness/features_1000.txt -g thickness/groups_1000.txt -w manhattan -n 50 -t False -o thickness/hiwenet_manhatten_n50.csv

Typical output can be seen in a file in the examples folder, called pairwise_histogram_dist.csv, which is shown below, wherein the upper triangular matrix is filled with the corresponding pair-wise distances:

0.000,0.903,0.882,0.859,0.865
0.000,0.000,0.910,0.916,0.914
0.000,0.000,0.000,0.902,0.903
0.000,0.000,0.000,0.000,0.945
0.000,0.000,0.000,0.000,0.000